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Reemst K, Shahin H, Shahar OD. Learning and memory formation in zebrafish: Protein dynamics and molecular tools. Front Cell Dev Biol 2023; 11:1120984. [PMID: 36968211 PMCID: PMC10034119 DOI: 10.3389/fcell.2023.1120984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Research on learning and memory formation at the level of neural networks, as well as at the molecular level, is challenging due to the immense complexity of the brain. The zebrafish as a genetically tractable model organism can overcome many of the current challenges of studying molecular mechanisms of learning and memory formation. Zebrafish have a translucent, smaller and more accessible brain than that of mammals, allowing imaging of the entire brain during behavioral manipulations. Recent years have seen an extensive increase in published brain research describing the use of zebrafish for the study of learning and memory. Nevertheless, due to the complexity of the brain comprising many neural cell types that are difficult to isolate, it has been difficult to elucidate neural networks and molecular mechanisms involved in memory formation in an unbiased manner, even in zebrafish larvae. Therefore, data regarding the identity, location, and intensity of nascent proteins during memory formation is still sparse and our understanding of the molecular networks remains limited, indicating a need for new techniques. Here, we review recent progress in establishing learning paradigms for zebrafish and the development of methods to elucidate neural and molecular networks of learning. We describe various types of learning and highlight directions for future studies, focusing on molecular mechanisms of long-term memory formation and promising state-of-the-art techniques such as cell-type-specific metabolic labeling.
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Affiliation(s)
- Kitty Reemst
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Heba Shahin
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Or David Shahar
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
- *Correspondence: Or David Shahar,
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Prabhakar P, Pielot R, Landgraf P, Wissing J, Bayrhammer A, van Ham M, Gundelfinger ED, Jänsch L, Dieterich DC, Müller A. Monitoring regional astrocyte diversity by cell type-specific proteomic labeling in vivo. Glia 2023; 71:682-703. [PMID: 36401581 DOI: 10.1002/glia.24304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
Astrocytes exhibit regional heterogeneity in morphology, function and molecular composition to support and modulate neuronal function and signaling in a region-specific manner. To characterize regional heterogeneity of astrocytic proteomes of different brain regions we established an inducible Aldh1l1-methionyl-tRNA-synthetaseL274G (MetRSL274G ) mouse line that allows astrocyte-specific metabolic labeling of newly synthesized proteins by azidonorleucine (ANL) in vivo and subsequent isolation of tagged proteins by click chemistry. We analyzed astrocytic proteins from four different brain regions by mass spectrometry. The induced expression of MetRSL274G is restricted to astrocytes and identified proteins show a high overlap with proteins compiled in "AstroProt," a newly established database for astrocytic proteins. Gene enrichment analysis reveals a high similarity among brain regions with subtle differences in enriched biological processes and in abundances of key astrocytic proteins for hippocampus, cortex and striatum. However, the cerebellar proteome stands out with proteins being highly associated with the calcium signaling pathway or with bipolar disorder. Subregional analysis of single astrocyte TAMRA intensities in hippocampal layers indicates distinct subregional heterogeneity of astrocytes and highlights the applicability of our toolbox to study differences of astrocytic proteomes in vivo.
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Affiliation(s)
- Priyadharshini Prabhakar
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Rainer Pielot
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Josef Wissing
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anne Bayrhammer
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Marco van Ham
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eckart D Gundelfinger
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Leibniz Institute for Neurobiology, RG Neuroplasticity, Magdeburg, Germany
| | - Lothar Jänsch
- Cellular Proteome Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Anke Müller
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
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Soykan T, Haucke V, Kuijpers M. Mechanism of synaptic protein turnover and its regulation by neuronal activity. Curr Opin Neurobiol 2021; 69:76-83. [PMID: 33744822 DOI: 10.1016/j.conb.2021.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/23/2022]
Abstract
Neurons are long-lived cells with a complex architecture, in which synapses may be located far away from the cell body and are subject to plastic changes, thereby posing special challenges to the systems that maintain and dynamically regulate the synaptic proteome. These mechanisms include neuronal autophagy and the endolysosome pathway, as well as the ubiquitin/proteasome system, which cooperate in the constitutive and regulated turnover of presynaptic and postsynaptic proteins. Here, we summarize the pathways involved in synaptic protein degradation and the mechanisms underlying their regulation, for example, by neuronal activity, with an emphasis on the presynaptic compartment and outline perspectives for future research. Keywords: Synapse, Synaptic vesicle, Autophagy, Endolysosome, Proteasome, Protein turnover, Protein degradation, Endosome, Lysosome.
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Affiliation(s)
- Tolga Soykan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195, Berlin, Germany.
| | - Marijn Kuijpers
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany.
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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